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ARS Home » Southeast Area » Miami, Florida » Subtropical Horticulture Research » Research » Publications at this Location » Publication #371237

Research Project: Development and Application of Genomic-assisted Breeding Strategies to Produce Disease-resistant Cacao Genetic Resources

Location: Subtropical Horticulture Research

Title: Establishment of cacao reference genotypes from different genetic groups using SNP markers

item Gutierrez, Osman
item Zhang, Dapeng
item TURNBULL, CHRIS - University Of Reading
item MOTAMAYOR, JUAN - Coca-Cola Company

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/23/2019
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Cacao (Theobroma cacao L.) is an important perennial crop for small farmers in tropical regions of the world whose center of origin and genetic diversity is the Amazon Basin. Improved understanding of population structure in cacao germplasm is important for cacao germplasm collecting, genebank management, and marker-trait association studies where the structured population causes false positive associations (or spurious associations). A core set of SNP markers, as well as a group of reference genotypes is urgently needed to properly classify cacao accessions that are currently present in several cacao collections worldwide. The goals of this study were to: (i) select cacao reference genotypes for each genetic group using single nucleotide polymorphism markers (ii) develop a SNP genotyping panel capable of differentiating genetic clusters of cacao germplasm. Five hundred and sixty-two selected accessions belonging to the known 10 cacao genetic groups (Amelonado, Contamana, Criollo, Curaray, Guiana, Iquitos, Marañon, Nacional, Nanay, and Purús) were screened using 1,060 single nucleotide polymorphic markers that are distributed across the 10 cacao chromosomes. A genotyping panel comprising 219 SNPs was selected based on call rate, minor allele frequency (MAF), Shannon’s information index and linkage disequilibrium (LD). Genetic distances based on this SNP panel is highly correlated with the previously reported result based on SSR markers. Result of population and sub-population classification largely agreed with the SSR-based classification, demonstrating the usefulness of this SNP panel in assessing genetic diversity and population structure in cacao. The selected genotypes from each genetic group with their SNP profiles and corresponding passport data will be deposited in public databases such as the International Cocoa Germplasm Database (ICGD) where they would serve as designated reference genotypes.